Autoimmune diseases affect about 5% of the human population, often causing chronic, debilitating illnesses. Although all individuals have immune cells that potentially react with antigens present on their own tissues, these autoreactive cells are normally held in check by complex and currently poorly understood regulatory mechanisms. In individuals who develop autoimmune disease, these regulatory mechanisms are proposed to be somehow defective, which allows autoreactive cells to mount an immunological attack against host tissues.
Animal models have aided in understanding the mechanisms underlying autoimmune diseases. For example, experimental allergic encephalomyelitis (EAE) is an autoimmune disease of the central nervous system that can be induced in mice and rats by immunization with myelin basic protein (MBP). Histologically and clinically, EAE resembles multiple sclerosis (MS) in humans. EAE is mediated by T cells having specificity for myelin antigens, such as MBP, as evidenced by the ability of MBP- or other myelin-reactive T cells to induce EAE when adoptively transferred to healthy hosts. Analysis of the antigen-binding receptor, or T cell receptor (TCR), expressed by MBP-reactive T cells has generally revealed that these T cells express a limited number of TCR V alpha (AV, α) and TCR V beta (BV, β) polypeptide chains.
The TCR is a heterodimeric glycoprotein present on the surface of T cells. The TCR exists in two forms, one consisting of an alpha chain and a beta chain, the second consisting of a gamma chain and a delta chain. Each TCR polypeptide chain is encoded by a genetic locus containing multiple discontinuous gene segments. These include variable (V) region gene segments, joining (J) region gene segments and constant (C) region gene segments. Beta and delta chains contain an additional element termed the diversity (D) gene segment. The TCR gene segments become rearranged during T cell maturation to form VJ or VDJ genes, which are then expressed as polypeptide chains. There are at least 50 different human Vα (or AV), 57-70 Vβ (or BV), 3 Vδ (or GV) and 7Vγ (or DV) gene segments, which are categorized into various families, with members of a family sharing substantial nucleotide and amino acid sequence identity.
EAE has successfully been prevented or treated by various methods that selectively target the TCR V genes present on encephalitogenic T cells. Such therapeutic methods include immunization with TCR V region peptides to induce an immune response against the autoreactive T cells, and administering anti-TCR V region antibodies to bind and either kill or inactivate the autoreactive T cells. Once the disease-associated TCR V genes are identified in humans, analogous immunotherapeutic methods that target T cells expressing these V genes are also expected to be effective. However, a need remains to provide an efficient and effective means to identify TCR V genes of use in therapeutic strategies.
Human autoimmune diseases have proven to be more complex than experimental animal models, in part because there are numerous autoantigens implicated in human diseases, and human responses to different autoantigens depend on multiple genetic factors. In certain studies, T cells from individuals with autoimmune disease that react to proposed autoantigens have been demonstrated to express a limited subset of V genes. However, the relevance of these T cells to the disease is as yet unclear, because the particular antigen used in assessing T cell reactivity is not necessarily involved in the etiology of the disease in that individual. In certain studies, T cells obtained from the site of the pathology from individuals with autoimmune disease have been demonstrated to express a limited subset of V genes. Unfortunately, the currently available methods of identifying TCR V gene usage do not take into account the regulatory mechanisms that may be acting in a particular individual to control the activity of the relevant T cells.
Thus, there exists a need for an improved method of identifying disease-associated T cells in individuals, including both autoreactive T cells and regulatory T cells. Once the identity of the disease-associated T cells is known, appropriate, individualized therapies can be selected to prevent or treat the disease. Thus, there also exists a need for assays to efficiently and effectively select therapeutic agents of use.